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H++ is an automated system that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools for analysis of electrostatic-related molecular properties. Why H++

If this is your first time using H++, please read the FAQ carefully.

H++ in more detail. Citations

Please report problems to the H++ team: ramu@vt.edu


7/2019 - H++ can now process structures with phosphorylated side chains. See FAQ.

7/2019 - FAQ has been updated to indicate that the c-terminus can be capped with an amide cap (-NH2), in addition to N-methylamide (NME) capping.

11/2018 - Fixed error encountered when processing a structure containing more than two CYS residues within 3A of each other.

11/2017 - Security and operating system upgrade to prevent unauthorized access to the H++ server

12/2016 - H++ can now calculate the pKs for proteins embedded in a membrane. See FAQ for details.

7/2015 - Most common ions can now be retained for pK calculations and will be included in the output topology/parameter and coordinate files. See FAQ for details.

7/2015 - H++ now uses the latest version of AmberTools and Amber force field parameters: AmberTools 15 using ff14SB force field parameters for proteins. with OL3 modifications for RNA, and OL1+OL4 modifications for DNA. See FAQ for details.

7/2015 - Water model option for solvent box. When generating an explicit solvent box, you can now select between two types of water models: OPC, a highly accurate 4-point water model, and TIP3P, the traditional 3-point water model. See [Izadi et. al., 2015, J Phys Chem Lett, 5(21), 3863-3871] for additional information on OPC.

5/2013 - The accuracy table for H++ has been updated to reflect a correction to experimental data used for comparison. The RMS error in calculated pK relative to experimental values is 1.0 pK units for a set of 23 protein structures with a total of 201 titratable groups. Refer to this link for more details.

NOTE: Current AMBER force fields in use: ff14SB force field parameters for proteins. with OL3 modifications for RNA, OL1+OL4 modifications for DNA, and the lipid11 modifications for lipids. See FAQ for details.